Quantitative Biology

Authors and titles for April 2020

[1] arXiv:2004.00056 [pdf, other]

Title: COVID-19 Outbreak in Pakistan: Model-Driven Impact Analysis and Guidelines

Kashif Zia, Umar Farooq

Comments: 12 pages, 6 figures

Subjects: Populations and Evolution (q-bio.PE); Optimization and Control (math.OC)

[2] arXiv:2004.00058 [pdf, other]

Title: A macro agent and its actions

Larissa Albantakis, Francesco Massari, Maggie Beheler-Amass, Giulio Tononi

Comments: 18 pages, 5 figures; to appear as a chapter in "Top-Down Causation and Emergence" published by Springer as part of the Synthese Library Book Series; F.M. and M.B. contributed equally to this work

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Neural and Evolutionary Computing (cs.NE); Quantitative Methods (q-bio.QM)

[3] arXiv:2004.00062 [pdf, other]

Title: On the comparison of incompatibility of split systems across different numbers of taxa

Michael Hendriksen, Nils Kapust

Comments: 9 pages, 2 figures. Updated to make writing and proofs clearer, some additional information included

Subjects: Populations and Evolution (q-bio.PE); Combinatorics (math.CO)

[4] arXiv:2004.00067 [pdf, other]

Title: Propagation and mitigation of epidemics in a scale-free network

Gyula M. Szabó

Comments: 8 pages, 5 figures. Currently submitted to ArXiv only and waiting for comments

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[5] arXiv:2004.00117 [pdf, other]

Title: Challenges in control of Covid-19: short doubling time and long delay to effect of interventions

Lorenzo Pellis, Francesca Scarabel, Helena B. Stage, Christopher E. Overton, Lauren H. K. Chappell, Katrina A. Lythgoe, Elizabeth Fearon, Emma Bennett, Jacob Curran-Sebastian, Rajenki Das, Martyn Fyles, Hugo Lewkowicz, Xiaoxi Pang, Bindu Vekaria, Luke Webb, Thomas House, Ian Hall

Comments: Main text: 13 pages (1-13), 3 figures, 1 table; Supplementary Information: 9 pages (14-22), 4 figures, 1 table

Subjects: Populations and Evolution (q-bio.PE)

[6] arXiv:2004.00156 [pdf, other]

Title: Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by Random Circuit Perturbation

Bin Huang, Mingyang Lu, Madeline Galbraith, Herbert Levine, Jose N. Onuchic, Dongya Jia

Comments: 28 pages, 8 figures

Subjects: Molecular Networks (q-bio.MN); Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM)

[7] arXiv:2004.00217 [pdf, other]

Title: Molecular docking studies on Jensenone from eucalyptus essential oil as a potential inhibitor of COVID 19 corona virus infection

Arun Dev Sharma, Inderjeet Kaur

Comments: 10 p. Research and reviews in biotechnology and biosciences 2020,7,59-66

Subjects: Biomolecules (q-bio.BM)

[8] arXiv:2004.00218 [pdf, other]

Title: 3D Deep Learning on Medical Images: A Review

Satya P. Singh, Lipo Wang, Sukrit Gupta, Haveesh Goli, Parasuraman Padmanabhan, Balázs Gulyás

Comments: Published in Sensors Journal (this https URL)

Journal-ref: Sensors 2020, 20, 5097

Subjects: Quantitative Methods (q-bio.QM); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG); Image and Video Processing (eess.IV)

[9] arXiv:2004.00261 [pdf, other]

Title: Five rules for friendly rivalry in direct reciprocity

Yohsuke Murase, Seung Ki Baek

Comments: 21 pages, 8 figures

Journal-ref: Sci. Rep. 10, 16904 (2020)

Subjects: Populations and Evolution (q-bio.PE)

[10] arXiv:2004.00351 [pdf, other]

Title: Machine learning a model for RNA structure prediction

Nicola Calonaci, Alisha Jones, Francesca Cuturello, Michael Sattler, Giovanni Bussi

Comments: Supporting Information are reported in a Jupyter notebook, in both format .pdf (read-only) and .ipynb (interactive and editable). Full data required to run the .ipynb notebook can be found at the GitHub repository reported in the notebook

Journal-ref: NAR Genom. Bioinform. 2, lqaa090 (2020)

Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph); Data Analysis, Statistics and Probability (physics.data-an); Quantitative Methods (q-bio.QM)

[11] arXiv:2004.00399 [pdf, other]

Title: Second-order Phase Transition in Phytoplankton Trait Dynamics

Jenny Held, Tom Lorimer, Francesco Pomati, Ruedi Stoop, Carlo Albert

Comments: Companion paper in BioRxiv this https URL

Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[12] arXiv:2004.00443 [pdf, other]

Title: Controlling the Transmission Dynamics of COVID-19

Stephen E. Moore, Eric Okyere

Comments: 13pages, 37 figures

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS); Optimization and Control (math.OC)

[13] arXiv:2004.00498 [pdf, other]

Title: Soft-wired long-term memory in a natural recurrent neuronal network

Miguel A. Casal, Santiago Galella, Oscar Vilarroya, Jordi Garcia-Ojalvo

Comments: 16 pages, 6 figures

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Chaotic Dynamics (nlin.CD); Biological Physics (physics.bio-ph)

[14] arXiv:2004.00552 [pdf, other]

Title: Development of swarm behavior in artificial learning agents that adapt to different foraging environments

Andrea López-Incera, Katja Ried, Thomas Müller, Hans J. Briegel

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG); Physics and Society (physics.soc-ph)

[15] arXiv:2004.00553 [pdf, other]

Title: Coronavirus Covid-19 spreading in Italy: optimizing an epidemiological model with dynamic social distancing through Differential Evolution

I. De Falco, A. Della Cioppa, U. Scafuri, E. Tarantino

Subjects: Populations and Evolution (q-bio.PE); Social and Information Networks (cs.SI); Physics and Society (physics.soc-ph)

[16] arXiv:2004.00579 [pdf, other]

Title: History of Onychophorology, 1826-2020

Julian Monge-Najera

Subjects: Other Quantitative Biology (q-bio.OT)

[17] arXiv:2004.00696 [pdf, other]

Title: Forecasting COVID 19 growth in India using Susceptible-Infected-Recovered (S.I.R) model

Jay Naresh Dhanwant, V. Ramanathan

Subjects: Populations and Evolution (q-bio.PE)

[18] arXiv:2004.00746 [pdf, other]

Title: Coronavirus SARS-CoV-2: Analysis of subgenomic mRNA transcription, 3CLpro and PL2pro protease cleavage sites and protein synthesis

Miguel Ramos Pascual

Subjects: Genomics (q-bio.GN)

[19] arXiv:2004.00834 [pdf, other]

Title: Inference of population genetic parameters with a biallelic mutation drift model using the coalescent, diffusion with orthogonal polynomials, and the Moran model

Claus Vogl, Sandra Peer

Comments: 26 pages, 2 figures

Subjects: Populations and Evolution (q-bio.PE)

[20] arXiv:2004.00914 [pdf, other]

Title: A comparative study between discrete and continuum models for the evolution of competing phenotype-structured cell populations in dynamical environments

Aleksandra Ardaševa, Robert A. Gatenby, Alexander R. A. Anderson, Helen M. Byrne, Philip K. Maini, Tommaso Lorenzi

Comments: 15 pages, 9 figures

Journal-ref: Phys. Rev. E 102, 042404 (2020)

Subjects: Populations and Evolution (q-bio.PE)

[21] arXiv:2004.00940 [pdf, other]

Title: Power-law distribution in the number of confirmed COVID-19 cases

Bernd Blasius

Comments: 10 pages, 8 figures; rewrite, emphasizing that the distribution is a truncated power law

Journal-ref: Chaos 30, 093123 (2020)

Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO)

[22] arXiv:2004.00958 [pdf, other]

Title: SEIR and Regression Model based COVID-19 outbreak predictions in India

Gaurav Pandey, Poonam Chaudhary, Rajan Gupta, Saibal Pal

Subjects: Populations and Evolution (q-bio.PE)

[23] arXiv:2004.00959 [pdf, other]

Title: Neural network based country wise risk prediction of COVID-19

Ratnabali Pal, Arif Ahmed Sekh, Samarjit Kar, Dilip K. Prasad

Journal-ref: Applied Sciences, 2020

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG)

[24] arXiv:2004.00979 [pdf, other]

Title: Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks

Markus Hofmarcher, Andreas Mayr, Elisabeth Rumetshofer, Peter Ruch, Philipp Renz, Johannes Schimunek, Philipp Seidl, Andreu Vall, Michael Widrich, Sepp Hochreiter, Günter Klambauer

Comments: Additional results added. Various corrections to formulations and typos

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)

[25] arXiv:2004.00987 [pdf, other]

Title: Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature

Francesco Bonazzi, Carol K. Hall, Thomas R. Weikl

Comments: 9 pages, 5 figures

Subjects: Subcellular Processes (q-bio.SC); Soft Condensed Matter (cond-mat.soft)

[26] arXiv:2004.00991 [pdf, other]

Title: Computational Performance of a Germline Variant Calling Pipeline for Next Generation Sequencing

Jie Liu, Xiaotian Wu, Kai Zhang, Bing Liu, Renyi Bao, Xiao Chen, Yiran Cai, Yiming Shen, Xinjun He, Jun Yan, Weixing Ji

Comments: 6 pages, 6 figures, 3 tables

Subjects: Genomics (q-bio.GN); Performance (cs.PF)

[27] arXiv:2004.00995 [pdf, other]

Title: Prediction of cellular burden with host-circuit models

Evangelos-Marios Nikolados, Andrea Y. Weiße, Diego A. Oyarzún

Subjects: Molecular Networks (q-bio.MN); Biomolecules (q-bio.BM); Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)

[28] arXiv:2004.01000 [pdf, other]

Title: A Bayesian approach to recover the theoretical temperature-dependent hatch date distribution from biased samples: the case of the common dolphinfish (Coryphaena hippurus)

Vicenç Moltó, Andres Ospina-Alvarez, Mark Gatt, Miquel Palmer, Ignacio A. Catalán

Comments: 7 pages, 2 figure, 2 appendices

Subjects: Other Quantitative Biology (q-bio.OT)

[29] arXiv:2004.01011 [pdf, other]

Title: Microbial populations under selection

Ellen Baake, Anton Wakolbinger

Comments: to appear in: Probabilistic Structures in Evolution, E.~Baake and A.~Wakolbinger (eds.), EMS Publishing House, Zurich

Journal-ref: in: Probabilistic Structures in Evolution (E. Baake, A. Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 43-68

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[30] arXiv:2004.01028 [pdf, other]

Title: DeepSIBA: Chemical Structure-based Inference of Biological Alterations

C. Fotis, N. Meimetis, A. Sardis, L.G. Alexopoulos

Comments: Article: 19 pages, Electronic Supplementary Information (included): 16 pages

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Machine Learning (stat.ML)

[31] arXiv:2004.01105 [pdf, other]

Title: Inferring change points in the COVID-19 spreading reveals the effectiveness of interventions

Jonas Dehning, Johannes Zierenberg, F. Paul Spitzner, Michael Wibral, Joao Pinheiro Neto, Michael Wilczek, Viola Priesemann

Comments: 23 pages, 11 figures. Our code is freely available and can be readily adapted to any country or region ( this https URL )

Journal-ref: Science 369, 160 (2020)

Subjects: Populations and Evolution (q-bio.PE)

[32] arXiv:2004.01114 [pdf, other]

Title: Anomalous subdiffusion in living cells: bridging the gap between experiments and realistic models through collaborative challenges

Maxime Woringer, Ignacio Izeddin, Cyril Favard, Hugues Berry

Comments: 10 pages, 1 figure

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[33] arXiv:2004.01154 [pdf, other]

Title: PEtab -- interoperable specification of parameter estimation problems in systems biology

Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

Subjects: Quantitative Methods (q-bio.QM)

[34] arXiv:2004.01207 [pdf, other]

Title: Estimation of population infected by Covid-19 using regression Generalized logistics and optimization heuristics

Mario Villalobos-Arias

Comments: 16 pages, 12 figures, prediction for covid-19, the document is in Spanish

Subjects: Populations and Evolution (q-bio.PE)

[35] arXiv:2004.01248 [pdf, other]

Title: Metropolitan-scale COVID-19 outbreaks: how similar are they?

Samuel Heroy

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[36] arXiv:2004.01295 [pdf, other]

Title: Different scenarios in the Dynamics of SARS-Cov-2 Infection: an adapted ODE model

Ramón E. R. González

Comments: 11 pages, 7 figures and 8 tables

Subjects: Populations and Evolution (q-bio.PE)

[37] arXiv:2004.01399 [pdf, other]

Title: Electrostatic precipitation of exhaled particles for tensiometric examination of pulmonary surfactant

Andrey Shmyrov, Alexey Mizev, Irina Mizeva, Anastasia Shmyrova

Comments: 19 pages, 6 figures, submitted

Subjects: Tissues and Organs (q-bio.TO); Biological Physics (physics.bio-ph)

[38] arXiv:2004.01453 [pdf, other]

Title: Alternating quarantine for sustainable epidemic mitigation

Dror Meidan, Nava Schulmann, Reuven Cohen, Simcha Haber, Eyal Yaniv, Ronit Sarid, Baruch Barzel

Comments: 36 pages, 13 figures

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[39] arXiv:2004.01574 [pdf, other]

Title: Analysis of the COVID-19 pandemic by SIR model and machine learning technics for forecasting

Babacar Mbaye Ndiaye, Lena Tendeng, Diaraf Seck

Subjects: Populations and Evolution (q-bio.PE); Optimization and Control (math.OC); Machine Learning (stat.ML)

[40] arXiv:2004.01575 [pdf, other]

Title: Model studies on the COVID-19 pandemic in Sweden

Chong Qi, Daniel Karlsson, Karl Sallmen, Ramon Wyss

Subjects: Populations and Evolution (q-bio.PE); Biological Physics (physics.bio-ph); Physics and Society (physics.soc-ph)

[41] arXiv:2004.01602 [pdf, other]

Title: Predicting rice blast disease: machine learning versus process based models

David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa Sarafijanovic-Djukic, Pau Puigdollers, Roberto Confalonieri

Journal-ref: BMC Bioinformatics volume 20, Article number: 514 (2019)

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Machine Learning (stat.ML)

[42] arXiv:2004.01634 [pdf, other]

Title: In Silico Screening of Some Naturally Occurring Bioactive Compounds Predicts Potential Inhibitors against SARS-COV-2 (COVID-19) Protease

Ashok Kumar Mishra, Satya Prakash Tewari

Comments: This research is dedicated to the peoples who have lost the lives, been struggling for the lives, been working hard to save the lives as well as been frightened for the lives while fighting against the pandemic COVID-19 i.e. the all CORONA WARRIORS

Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)

[43] arXiv:2004.01665 [pdf, other]

Title: Present and future frameworks of theoretical neuroscience: outcomes of a community discussion

Horacio G. Rotstein, Fidel Santamaria

Comments: Workshop outcomes, 9 pages

Subjects: Neurons and Cognition (q-bio.NC)

[44] arXiv:2004.01710 [pdf, other]

Title: Characterizing Halloumi cheese bacterial communities through metagenomic analysis

Eleni Kamilari, Dimitrios A. Anagnostopoulos, Photis Papademas, Andreas Kamilaris, Dimitris Tsaltas

Journal-ref: LWT (2020): 109298

Subjects: Genomics (q-bio.GN); Computers and Society (cs.CY)

[45] arXiv:2004.01714 [pdf, other]

Title: Analyzing the World-Wide Impact of Public Health Interventions on the Transmission Dynamics of COVID-19

George Mohler, Frederic Schoenberg, Martin B. Short, Daniel Sledge

Subjects: Populations and Evolution (q-bio.PE)

[46] arXiv:2004.01805 [pdf, other]

Title: Accounting for Symptomatic and Asymptomatic in a SEIR-type model of COVID-19

Jayrold P. Arcede, Randy L. Caga-anan, Cheryl Q. Mentuda, Youcef Mammeri

Subjects: Populations and Evolution (q-bio.PE)

[47] arXiv:2004.01819 [pdf, other]

Title: DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approach

Rifat Zahan, Ian McQuillan, Nathaniel D. Osgood

Journal-ref: In 2018 IEEE International Conference on Healthcare Informatics (ICHI) (pp. 363-365). IEEE (2018, June)

Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG); Machine Learning (stat.ML)

[48] arXiv:2004.01966 [pdf, other]

Title: Facultative predation can alter the ant-aphid population

Atsuki Nakai, Yoko Inui, Kei Tokita

Comments: 28 pages, 6 figures

Subjects: Populations and Evolution (q-bio.PE)

[49] arXiv:2004.01974 [pdf, other]

Title: COVID-19: Development of a Robust Mathematical Model and Simulation Package with Consideration for Ageing Population and Time Delay for Control Action and Resusceptibility

Kok Yew Ng, Meei Mei Gui

Comments: 14 pages, 9 figures, To appear in Physica D: Nonlinear Phenomena (2020)

Journal-ref: Physica D: Nonlinear Phenomena (2020)

Subjects: Populations and Evolution (q-bio.PE)

[50] arXiv:2004.02006 [pdf, other]

Title: Stochastic and nonstochastic descriptions of the 2019-2020 measles outbreak worldwide with an emphasis in Mexico

A. Vivanco-Lira, R. Luna-Banenelli

Comments: 31 pages, 11 figures

Subjects: Populations and Evolution (q-bio.PE); Cell Behavior (q-bio.CB)